Non-helically perturbed polymers are a product of pairwise reduction along symmetry lines of uneven Bessel orders. The result is a discontinuity in the form of a helical seam. Seams have been shown to occur in TMV [1], microtubules [2] and bacterial flagellar filaments [3]. Only the structure of seamed microtubules was fully analyzed.
The right-handed flagellar filament of Salmonella typhimurium sjw23 (serotype gt) is non-helically perturbed. removing the outer, D3, flagellin domain from the fliC23 gene or replacing it with a domain from an unperturbed strain (sjw1655) restores helical symmetry (as indicated by the disappearance of the typical layer-line clusters (n= -2.5, -13.5, 8.5) from the power spectrum). This suggests that the non-helical perturbation is, likely, a product of unique interactions in the inner part of the outer D2/D3 domains. To specify the sub-molecular interactions leading to the perturbation, we need a full three-dimensional reconstruction.
Microtubules are assembled from globular alpha and beta tubulin dimers, are thin-walled, hollow tubes with long, nearly vertical, helical repeats. bacterial flagellar filaments, in comparison, are dense polymers with a narrow central channel and a complex, four domained radial mass distribution.
using the underlying symmetry of the perturbed filament we develop a streamlined, compact and efficient reconstruction procedure. It is based on the long range helical order of the seam and the shorter repeats as ‘single particles’. We utilize the short helical repeat (n=11, 393Å) and the long helical repeat of the seam (393x11=4323Å). The method, compared to microtubule reconstructions, (1) does not require an external reference, (2) does not require prior knowledge of the location of the seam, (3) can handle short independent segments as single particles, (4) helical averaging of the protofilaments is done in one step and (5) brings into account the relation between the seam ‘s angular position and the tube’s radius. Determining the polymer`s symmetry allows restoring, or ‘reverse engineering’ helicity so as to compensate for the perturbation and reconstruct the structure. The perturbation can be reconstructed as a straight or helical seam.
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[3] K. Nisani-Bizer, S. Trachtenberg, Unperturbing a non-helically perturbed bacterial flagellar filament: Salmonella typhimurium SJW23, J. Mol. Biol. 416 (2012) 367–388. doi:10.1016/j.jmb.2012.01.003.
[4] D.L. Caspar, K.C. Holmes, Structure of dahlemense strain of tobacco mosaic virus: a periodically deformed helix., J. Mol. Biol. 46 (1969) 99–133. http://www.ncbi.nlm.nih.gov/pubmed/5358645 (accessed August 22, 2016).
